@pipeworx/ucsc-genome

Reference genome assemblies from the UCSC Genome Browser — which builds exist for a species, which annotation tracks sit on each build, the actual rows of any track over a genomic interval, and raw reference DNA.

Part of Pipeworx — an MCP gateway connecting AI agents to 1684+ live data sources.

Tools

• ucsc_genomes(search?, limit?) — every UCSC assembly (~238), with its assembly ID (hg38, mm39, danRer11), organism, scientific name, source assembly and release description. This is where you get the ID every other call keys on.
• ucsc_tracks(genome, search?, limit?) — annotation tracks on one assembly, with the INTERNAL track name that ucsc_track_data wants. The browser UI shows labels, not names: "GENCODE V50" is track knownGene, and there is no rule that maps one to the other.
• ucsc_track_data(genome, track, chrom, start, end, maxItemsOutput?) — the track's rows over an interval: gene models with exon structure, ClinVar variants, repeats, whatever that track holds.
• ucsc_sequence(genome, chrom, start, end, revComp?) — reference DNA for an interval, with GC fraction and an N count.

Auth

Keyless. No registration, no rate-limit headers observed. UCSC asks heavy users to mirror or use a local install rather than hammer the public endpoint, so keep interval widths sane.

Data sources

• https://api.genome.ucsc.edu/list/ucscGenomes — assembly catalogue.
• https://api.genome.ucsc.edu/list/tracks?genome=hg38 — track catalogue for one assembly.
• https://api.genome.ucsc.edu/getData/track — track rows over an interval.
• https://api.genome.ucsc.edu/getData/sequence — reference DNA.
• Docs: https://genome.ucsc.edu/goldenPath/help/api.html

Traps

genome is required on every coordinate tool and there is no default. hg19 (GRCh37) and hg38 (GRCh38) are different coordinate systems for the same genome, and every position is valid in both — so a wrong build never errors, it returns confident annotations for a different locus. BRCA1 sits at chr17:41,196,311-41,277,500 in hg19 and chr17:43,044,295-43,170,245 in hg38. Anything older than ~2018 (published tables, clinical spreadsheets, most dbSNP dumps) is hg19.

Coordinates are 0-based half-open; the Genome Browser UI is 1-based inclusive. A position copied out of the browser location box is one too high at the start.

Chromosomes need the chr prefix. UCSC wants chr17; Ensembl/NCBI style bare 17 is rejected.

Track search ranks by where the match landed, on purpose. hg38 carries ~24,000 tracks (most of them ENCODE subtracks) and the longLabels are prose, so a plain substring search for "gencode" matched 13,427 of them — and ~13,000 of those were false positives, because wgEncodeBroadHistone… lowercases to a string that literally contains "gencode". The ranking scores an internal-name hit above a shortLabel hit above prose, and treats a camelCase transition as a word boundary, which is what separates nmdEscGencode from wgEncode…. Without it the answer (knownGene) was on page 2,700.

Composite tracks nest their subtracks one level down inside the parent object. ucsc_tracks flattens them, otherwise a search for "clinvar" on hg38 misses every subtrack of the ClinVar container and reads as "UCSC does not have ClinVar".

getData/track keys its row array on the track name — usually. On some composites it keys on a subtrack instead, so the pack falls back to "the first array in the response" rather than reporting an empty result that is really a naming mismatch.

A bad assembly or track returns HTTP 400 with a useful error string in the JSON body — the pack surfaces that string, because "hg19 is not a valid track for genome hg38" is the whole diagnosis.

Quick Start

Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):

{
  "mcpServers": {
    "ucsc-genome": {
      "url": "https://gateway.pipeworx.io/ucsc-genome/mcp"
    }
  }
}

What this endpoint actually serves

tools/list at https://gateway.pipeworx.io/ucsc-genome/mcp returns the tools in the table above plus the shared Pipeworx meta-tools — ask_pipeworx, discover_tools, search_within, remember/recall and the rest of the gateway-wide set. So the tool count you see is larger than this table: a single-pack endpoint currently lists roughly 30 shared tools alongside the pack's own. The connection's initialize response states its exact scope, and is the authoritative answer for a given day.

This is deliberate, not multiplexing by accident. The meta-tools are what let a scoped connection answer a question this pack does not cover — via ask_pipeworx, which routes across the whole catalog — without you adding a second MCP server. There is currently no way to mount a pack endpoint without them; if the extra schemas cost you more context than the routing is worth, connect to the full gateway once rather than to several pack endpoints.

Or connect to the full Pipeworx gateway to get every pack's tools listed directly, instead of just this one's:

{
  "mcpServers": {
    "pipeworx": {
      "url": "https://gateway.pipeworx.io/mcp"
    }
  }
}

Both URLs reach the same gateway and the same 1684+ data sources. The only difference is which pack's tools are listed directly; ask_pipeworx reaches all of them from either one.

No MCP client? Call it over HTTP

curl -X POST https://gateway.pipeworx.io/v1/tools/ucsc_genomes \
  -H 'Content-Type: application/json' \
  -d '{"search":"human"}'

No account needed for the first calls. Inspect any tool: GET https://gateway.pipeworx.io/v1/tools/ucsc_genomes. Find one: POST https://gateway.pipeworx.io/v1/tools/search_packs with {"query":"..."}.

Standalone (no gateway account)

This package also runs as a local stdio MCP server — no Pipeworx account, no gateway round-trip:

{
  "mcpServers": {
    "ucsc-genome": {
      "command": "npx",
      "args": ["-y", "@pipeworx/mcp-ucsc-genome"]
    }
  }
}

Or run it directly to confirm it starts:

npx -y @pipeworx/mcp-ucsc-genome

It speaks MCP over stdin/stdout and answers initialize/tools/list/tools/call for only this pack's tools — none of the shared meta-tools the gateway connection above adds. Same source, same tools, no ask_pipeworx routing.

Using with ask_pipeworx

Instead of calling tools directly, you can ask questions in plain English — this works on the pack endpoint above as well as on the full gateway:

ask_pipeworx({ question: "your question about Ucsc Genome data" })

The gateway picks the right tool and fills the arguments automatically.

More

• Docs and guides
• pipeworx.io

License

MIT